
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   45 (  180),  selected   45 , name T0363AL242_4-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL242_4-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N      11           -
LGA    -       -      Q      12           -
LGA    Q      12      I      13          1.164
LGA    I      13      N      14          2.653
LGA    N      14      I      15          1.892
LGA    I      15      E      16          0.651
LGA    E      16      I      17          3.387
LGA    I      17      A      18          1.521
LGA    A      18      Y      19          3.376
LGA    Y      19      A      20          1.642
LGA    A      20      F      21          0.587
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    F      21      R      24           #
LGA    P      22      Y      25          2.650
LGA    E      23      Y      26          4.689
LGA    R      24      -       -           -
LGA    Y      25      -       -           -
LGA    Y      26      -       -           -
LGA    L      27      -       -           -
LGA    K      28      L      27          2.487
LGA    S      29      K      28          2.823
LGA    F      30      S      29          1.169
LGA    Q      31      F      30          2.434
LGA    V      32      Q      31          1.882
LGA    D      33      V      32          1.811
LGA    E      34      D      33          2.764
LGA    G      35      E      34          4.335
LGA    I      36      G      35          4.771
LGA    T      37      I      36          3.286
LGA    V      38      T      37          1.461
LGA    Q      39      V      38          0.776
LGA    T      40      Q      39          0.802
LGA    A      41      T      40          1.075
LGA    I      42      A      41          1.110
LGA    T      43      I      42          1.133
LGA    Q      44      T      43          1.340
LGA    S      45      Q      44          0.891
LGA    G      46      S      45          0.689
LGA    I      47      G      46          1.983
LGA    L      48      -       -           -
LGA    S      49      -       -           -
LGA    Q      50      I      47          3.358
LGA    F      51      L      48          3.354
LGA    P      52      S      49          2.871
LGA    E      53      Q      50          3.520
LGA    I      54      F      51          5.131
LGA    D      55      P      52          4.556
LGA    L      56      E      53          3.370
LGA    -       -      I      54           -
LGA    -       -      D      55           -
LGA    -       -      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   45   46    5.0     38    2.68     0.00     52.511     1.365

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.594584 * X  +   0.777835 * Y  +   0.203575 * Z  +  12.662408
  Y_new =  -0.134719 * X  +  -0.345992 * Y  +   0.928515 * Z  +  27.722481
  Z_new =   0.792667 * X  +   0.524654 * Y  +   0.310510 * Z  + -23.279715 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.036400   -2.105193  [ DEG:    59.3813   -120.6187 ]
  Theta =  -0.915171   -2.226421  [ DEG:   -52.4355   -127.5645 ]
  Phi   =  -2.918777    0.222815  [ DEG:  -167.2336     12.7664 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0363AL242_4-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL242_4-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   45   46   5.0   38   2.68    0.00  52.511
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL242_4-D1
REMARK Aligment from pdb entry: 1fm0_D
ATOM      1  N   GLN    12      15.224   6.288   8.041  1.00  0.00              
ATOM      2  CA  GLN    12      16.586   6.536   7.486  1.00  0.00              
ATOM      3  C   GLN    12      17.130   7.856   8.001  1.00  0.00              
ATOM      4  O   GLN    12      16.410   8.590   8.678  1.00  0.00              
ATOM      5  N   ILE    13      18.419   8.104   7.752  1.00  0.00              
ATOM      6  CA  ILE    13      18.987   9.450   7.930  1.00  0.00              
ATOM      7  C   ILE    13      19.195  10.244   6.595  1.00  0.00              
ATOM      8  O   ILE    13      19.803   9.727   5.646  1.00  0.00              
ATOM      9  N   ASN    14      18.660  11.494   6.550  1.00  0.00              
ATOM     10  CA  ASN    14      18.756  12.408   5.373  1.00  0.00              
ATOM     11  C   ASN    14      20.002  13.289   5.532  1.00  0.00              
ATOM     12  O   ASN    14      20.184  13.895   6.598  1.00  0.00              
ATOM     13  N   ILE    15      20.840  13.336   4.492  1.00  0.00              
ATOM     14  CA  ILE    15      22.107  14.111   4.480  1.00  0.00              
ATOM     15  C   ILE    15      22.065  15.174   3.372  1.00  0.00              
ATOM     16  O   ILE    15      21.815  14.861   2.197  1.00  0.00              
ATOM     17  N   GLU    16      22.278  16.432   3.773  1.00  0.00              
ATOM     18  CA  GLU    16      22.304  17.606   2.890  1.00  0.00              
ATOM     19  C   GLU    16      23.724  18.197   2.768  1.00  0.00              
ATOM     20  O   GLU    16      24.507  18.132   3.715  1.00  0.00              
ATOM     21  N   ILE    17      24.017  18.783   1.597  1.00  0.00              
ATOM     22  CA  ILE    17      25.322  19.401   1.294  1.00  0.00              
ATOM     23  C   ILE    17      25.141  20.833   0.756  1.00  0.00              
ATOM     24  O   ILE    17      24.142  21.113   0.075  1.00  0.00              
ATOM     25  N   ALA    18      26.107  21.721   1.025  1.00  0.00              
ATOM     26  CA  ALA    18      26.058  23.127   0.572  1.00  0.00              
ATOM     27  C   ALA    18      27.385  23.646   0.002  1.00  0.00              
ATOM     28  O   ALA    18      28.468  23.130   0.322  1.00  0.00              
ATOM     29  N   TYR    19      27.281  24.656  -0.872  1.00  0.00              
ATOM     30  CA  TYR    19      28.419  25.387  -1.437  1.00  0.00              
ATOM     31  C   TYR    19      29.481  24.460  -2.071  1.00  0.00              
ATOM     32  O   TYR    19      29.113  23.557  -2.831  1.00  0.00              
ATOM     33  N   ALA    20      30.766  24.659  -1.798  1.00  0.00              
ATOM     34  CA  ALA    20      31.828  23.836  -2.417  1.00  0.00              
ATOM     35  C   ALA    20      31.661  22.345  -2.137  1.00  0.00              
ATOM     36  O   ALA    20      32.069  21.502  -2.955  1.00  0.00              
ATOM     37  N   PHE    21      31.160  22.003  -0.944  1.00  0.00              
ATOM     38  CA  PHE    21      30.955  20.600  -0.593  1.00  0.00              
ATOM     39  C   PHE    21      29.941  19.957  -1.555  1.00  0.00              
ATOM     40  O   PHE    21      30.187  18.877  -2.117  1.00  0.00              
ATOM     41  N   PRO    22      28.796  20.626  -1.733  1.00  0.00              
ATOM     42  CA  PRO    22      27.753  20.205  -2.674  1.00  0.00              
ATOM     43  C   PRO    22      28.282  20.028  -4.102  1.00  0.00              
ATOM     44  O   PRO    22      27.977  19.026  -4.778  1.00  0.00              
ATOM     45  N   GLU    23      29.072  21.000  -4.558  1.00  0.00              
ATOM     46  CA  GLU    23      29.644  20.965  -5.916  1.00  0.00              
ATOM     47  C   GLU    23      30.549  19.734  -6.111  1.00  0.00              
ATOM     48  O   GLU    23      30.439  19.034  -7.129  1.00  0.00              
ATOM     49  N   ARG    24      31.393  19.437  -5.127  1.00  0.00              
ATOM     50  CA  ARG    24      32.332  18.319  -5.253  1.00  0.00              
ATOM     51  C   ARG    24      31.651  16.951  -5.088  1.00  0.00              
ATOM     52  O   ARG    24      31.948  16.000  -5.840  1.00  0.00              
ATOM     53  N   TYR    25      30.732  16.805  -4.127  1.00  0.00              
ATOM     54  CA  TYR    25      30.065  15.496  -3.975  1.00  0.00              
ATOM     55  C   TYR    25      29.128  15.205  -5.162  1.00  0.00              
ATOM     56  O   TYR    25      28.876  14.041  -5.487  1.00  0.00              
ATOM     57  N   TYR    26      28.604  16.255  -5.807  1.00  0.00              
ATOM     58  CA  TYR    26      27.798  16.066  -7.007  1.00  0.00              
ATOM     59  C   TYR    26      26.313  15.802  -6.843  1.00  0.00              
ATOM     60  O   TYR    26      25.649  15.397  -7.816  1.00  0.00              
ATOM     61  N   LEU    27      25.805  16.020  -5.635  1.00  0.00              
ATOM     62  CA  LEU    27      24.385  15.885  -5.332  1.00  0.00              
ATOM     63  C   LEU    27      24.054  16.859  -4.199  1.00  0.00              
ATOM     64  O   LEU    27      24.929  17.203  -3.402  1.00  0.00              
ATOM     65  N   LYS    28      22.792  17.290  -4.118  1.00  0.00              
ATOM     66  CA  LYS    28      22.336  18.204  -3.068  1.00  0.00              
ATOM     67  C   LYS    28      21.898  17.478  -1.785  1.00  0.00              
ATOM     68  O   LYS    28      21.893  18.085  -0.689  1.00  0.00              
ATOM     69  N   SER    29      21.535  16.199  -1.908  1.00  0.00              
ATOM     70  CA  SER    29      20.924  15.462  -0.803  1.00  0.00              
ATOM     71  C   SER    29      20.937  13.969  -1.084  1.00  0.00              
ATOM     72  O   SER    29      20.800  13.560  -2.248  1.00  0.00              
ATOM     73  N   PHE    30      21.064  13.159  -0.036  1.00  0.00              
ATOM     74  CA  PHE    30      20.958  11.696  -0.171  1.00  0.00              
ATOM     75  C   PHE    30      20.489  11.068   1.148  1.00  0.00              
ATOM     76  O   PHE    30      20.426  11.730   2.182  1.00  0.00              
ATOM     77  N   GLN    31      20.117   9.792   1.103  1.00  0.00              
ATOM     78  CA  GLN    31      19.638   9.063   2.283  1.00  0.00              
ATOM     79  C   GLN    31      20.584   7.928   2.645  1.00  0.00              
ATOM     80  O   GLN    31      21.155   7.293   1.750  1.00  0.00              
ATOM     81  N   VAL    32      20.744   7.676   3.946  1.00  0.00              
ATOM     82  CA  VAL    32      21.565   6.582   4.461  1.00  0.00              
ATOM     83  C   VAL    32      20.810   5.832   5.580  1.00  0.00              
ATOM     84  O   VAL    32      20.024   6.415   6.322  1.00  0.00              
ATOM     85  N   ASP    33      21.007   4.521   5.705  1.00  0.00              
ATOM     86  CA  ASP    33      20.385   3.792   6.815  1.00  0.00              
ATOM     87  C   ASP    33      20.888   4.343   8.169  1.00  0.00              
ATOM     88  O   ASP    33      21.951   4.969   8.245  1.00  0.00              
ATOM     89  N   GLU    34      20.143   4.106   9.245  1.00  0.00              
ATOM     90  CA  GLU    34      20.558   4.617  10.554  1.00  0.00              
ATOM     91  C   GLU    34      21.494   3.642  11.283  1.00  0.00              
ATOM     92  O   GLU    34      21.208   3.219  12.408  1.00  0.00              
ATOM     93  N   GLY    35      22.618   3.320  10.642  1.00  0.00              
ATOM     94  CA  GLY    35      23.606   2.389  11.185  1.00  0.00              
ATOM     95  C   GLY    35      24.924   3.045  11.589  1.00  0.00              
ATOM     96  O   GLY    35      25.975   2.424  11.443  1.00  0.00              
ATOM     97  N   ILE    36      24.892   4.285  12.063  1.00  0.00              
ATOM     98  CA  ILE    36      26.121   4.950  12.491  1.00  0.00              
ATOM     99  C   ILE    36      25.915   5.636  13.845  1.00  0.00              
ATOM    100  O   ILE    36      24.941   6.364  14.026  1.00  0.00              
ATOM    101  N   THR    37      26.822   5.396  14.797  1.00  0.00              
ATOM    102  CA  THR    37      26.659   5.947  16.148  1.00  0.00              
ATOM    103  C   THR    37      26.763   7.479  16.272  1.00  0.00              
ATOM    104  O   THR    37      26.080   8.062  17.105  1.00  0.00              
ATOM    105  N   VAL    38      27.576   8.109  15.428  1.00  0.00              
ATOM    106  CA  VAL    38      27.841   9.553  15.510  1.00  0.00              
ATOM    107  C   VAL    38      27.971  10.215  14.141  1.00  0.00              
ATOM    108  O   VAL    38      28.090   9.539  13.112  1.00  0.00              
ATOM    109  N   GLN    39      27.959  11.553  14.149  1.00  0.00              
ATOM    110  CA  GLN    39      28.222  12.337  12.941  1.00  0.00              
ATOM    111  C   GLN    39      29.582  11.930  12.318  1.00  0.00              
ATOM    112  O   GLN    39      29.708  11.787  11.095  1.00  0.00              
ATOM    113  N   THR    40      30.615  11.786  13.153  1.00  0.00              
ATOM    114  CA  THR    40      31.954  11.404  12.653  1.00  0.00              
ATOM    115  C   THR    40      31.960  10.045  11.940  1.00  0.00              
ATOM    116  O   THR    40      32.598   9.897  10.889  1.00  0.00              
ATOM    117  N   ALA    41      31.280   9.050  12.509  1.00  0.00              
ATOM    118  CA  ALA    41      31.192   7.734  11.857  1.00  0.00              
ATOM    119  C   ALA    41      30.505   7.835  10.486  1.00  0.00              
ATOM    120  O   ALA    41      30.937   7.195   9.525  1.00  0.00              
ATOM    121  N   ILE    42      29.431   8.637  10.406  1.00  0.00              
ATOM    122  CA  ILE    42      28.764   8.895   9.118  1.00  0.00              
ATOM    123  C   ILE    42      29.712   9.615   8.114  1.00  0.00              
ATOM    124  O   ILE    42      29.789   9.234   6.944  1.00  0.00              
ATOM    125  N   THR    43      30.418  10.650   8.580  1.00  0.00              
ATOM    126  CA  THR    43      31.383  11.384   7.742  1.00  0.00              
ATOM    127  C   THR    43      32.428  10.422   7.138  1.00  0.00              
ATOM    128  O   THR    43      32.714  10.452   5.918  1.00  0.00              
ATOM    129  N   GLN    44      32.983   9.540   7.975  1.00  0.00              
ATOM    130  CA  GLN    44      34.005   8.570   7.505  1.00  0.00              
ATOM    131  C   GLN    44      33.412   7.610   6.444  1.00  0.00              
ATOM    132  O   GLN    44      34.054   7.293   5.446  1.00  0.00              
ATOM    133  N   SER    45      32.200   7.105   6.691  1.00  0.00              
ATOM    134  CA  SER    45      31.530   6.223   5.726  1.00  0.00              
ATOM    135  C   SER    45      31.339   6.901   4.359  1.00  0.00              
ATOM    136  O   SER    45      31.619   6.299   3.306  1.00  0.00              
ATOM    137  N   GLY    46      30.854   8.145   4.377  1.00  0.00              
ATOM    138  CA  GLY    46      30.616   8.867   3.122  1.00  0.00              
ATOM    139  C   GLY    46      31.940   9.211   2.400  1.00  0.00              
ATOM    140  O   GLY    46      32.034   9.092   1.157  1.00  0.00              
ATOM    141  N   ILE    47      32.969   9.618   3.158  1.00  0.00              
ATOM    142  CA  ILE    47      34.284   9.914   2.569  1.00  0.00              
ATOM    143  C   ILE    47      34.878   8.692   1.847  1.00  0.00              
ATOM    144  O   ILE    47      35.634   8.834   0.871  1.00  0.00              
ATOM    145  N   LEU    48      37.060   9.100  -4.374  1.00  0.00              
ATOM    146  CA  LEU    48      38.111  10.089  -4.168  1.00  0.00              
ATOM    147  C   LEU    48      37.530  11.515  -4.078  1.00  0.00              
ATOM    148  O   LEU    48      38.031  12.329  -3.302  1.00  0.00              
ATOM    149  N   SER    49      36.482  11.812  -4.858  1.00  0.00              
ATOM    150  CA  SER    49      35.827  13.135  -4.800  1.00  0.00              
ATOM    151  C   SER    49      35.114  13.338  -3.459  1.00  0.00              
ATOM    152  O   SER    49      35.177  14.430  -2.889  1.00  0.00              
ATOM    153  N   GLN    50      34.405  12.310  -2.978  1.00  0.00              
ATOM    154  CA  GLN    50      33.724  12.396  -1.678  1.00  0.00              
ATOM    155  C   GLN    50      34.747  12.561  -0.530  1.00  0.00              
ATOM    156  O   GLN    50      34.512  13.311   0.409  1.00  0.00              
ATOM    157  N   PHE    51      35.903  11.887  -0.635  1.00  0.00              
ATOM    158  CA  PHE    51      36.954  12.033   0.389  1.00  0.00              
ATOM    159  C   PHE    51      37.516  13.464   0.431  1.00  0.00              
ATOM    160  O   PHE    51      37.705  14.044   1.504  1.00  0.00              
ATOM    161  N   PRO    52      37.773  14.046  -0.741  1.00  0.00              
ATOM    162  CA  PRO    52      38.280  15.409  -0.792  1.00  0.00              
ATOM    163  C   PRO    52      37.281  16.409  -0.196  1.00  0.00              
ATOM    164  O   PRO    52      37.657  17.313   0.562  1.00  0.00              
ATOM    165  N   GLU    53      36.003  16.233  -0.517  1.00  0.00              
ATOM    166  CA  GLU    53      34.954  17.129  -0.010  1.00  0.00              
ATOM    167  C   GLU    53      34.751  17.067   1.504  1.00  0.00              
ATOM    168  O   GLU    53      34.468  18.093   2.134  1.00  0.00              
ATOM    169  N   ILE    54      34.853  15.863   2.061  1.00  0.00              
ATOM    170  CA  ILE    54      34.511  15.620   3.458  1.00  0.00              
ATOM    171  C   ILE    54      35.679  15.419   4.432  1.00  0.00              
ATOM    172  O   ILE    54      35.448  15.234   5.617  1.00  0.00              
ATOM    173  N   ASP    55      36.928  15.453   3.963  1.00  0.00              
ATOM    174  CA  ASP    55      38.081  15.289   4.877  1.00  0.00              
ATOM    175  C   ASP    55      38.759  16.618   5.269  1.00  0.00              
ATOM    176  O   ASP    55      39.802  16.622   5.946  1.00  0.00              
ATOM    177  N   LEU    56      38.179  17.748   4.868  1.00  0.00              
ATOM    178  CA  LEU    56      38.737  19.056   5.214  1.00  0.00              
ATOM    179  C   LEU    56      38.658  19.383   6.721  1.00  0.00              
ATOM    180  O   LEU    56      37.625  19.198   7.357  1.00  0.00              
END
